anyhow, I know its an ancient ship, but still, something makes me wish Dr. McKay and Shepard were there..

Heh, you and me both. McKay should have been able to get everyone back home by the end of the pilot episode. But if for some reason he didn't, than Sheppard would have had the balls to carry though and vent the gate room of its atmosphere when the Lucian Alliance boarded.

But anyhoo, Atlantis was an amazing show in its first two seasons. They did some really great stuff back then and at time (especially in the first) it reminded me of Star Trek's good old days. Yes, I did intend to say Star Trek, watching Atlantis episode from the first half of the first season reminded me of way back one upon a time when I first began watching TNG.

Unfortunately, by the time they got to the third season they were starting to run out of ideas. And the ideas they had they weren't doing anything with. The Michael storyline was a mess which had the potential to be somewhat decent, never really seemed to amount to anything. And the less said about the Replicators the better.

The fourth season suffered from unnecessary changes, most notably among the cast, and by now they were resorting to tired old sci-fi cliches for episodes or recycling SG-1 episodes with the characters acknowledging they were recycling SG-1 episodes, like in Doppleganger compared to SG-1's Cold Lazarus.

Atlantis began puling itself together in its fifth season but unfortunately by then it was too little too late.

they could do some wild stuff, like make the atlantis city just a small part, and find add-ons that were previously lost, or explore new things from the secret janus lab, there is so much potential there, and not to mention the lost asgard storylines..

The potential to do this has always existed in Atlantis, it was just squandered in favour of doing other things like bring the Replicators back from their 15th extinction.